My father is on long-term use of oral prednisone for an inflammatory arthritis (polymyalgia rheumatica), and currently tapering (I am one a caregiver). Stomach upset is a known side effect, so there are specific instructions to take it only with food. I don't know that it would change "gastric structure" though. It does have many side effects because it affects hormones, neurotransmitters, and the immune system--all things which could impact GI symptoms, mood, etc., so it's usually prescribed very intentionally and with a time frame. That said, he hasn't had any GI symptoms, but he always takes his dose with food.